Biology subjects

Leveque, G.

Publications and source records attributed to Leveque, G..

3 recordsLinked to original sources

bioRxiv2025

A framework for integrating genomic profiles into captive breeding and reinforcement programmes: A case study on captive saker falcons

Ex-situ conservation is crucial for preserving endangered species by breeding to preserve genetic diversity and provide surplus for translocation, thereby supporting in-situ conservation and enhancing wild populations. Genomic tools can assist breeding strategies and ensure long-term success of ex-situ conservation efforts by assessing genetic introgression, determining genetic origin and status, and inferring genetic relatedness of potential founders. This study aims to develop a comprehensive genomic approach for assessing the genetic profiles of candidate founders for ex-situ breeding, with the goal of releasing surplus individuals while using the endangered Saker Falcons (Falco cherrug) as a study model. Genetic clustering of 31 captive sakers revealed both diverse origins, some matching wild Asian individuals (Mongolia), and a lineage (Group III) divergent from wild populations. Comparative analyses detected hybridisation signals in 61.3% of individuals, including three with gyrfalcon (F. rusticolus) introgression and Group IIIs pronounced divergence indicating past interbreeding with an unknown falcon species. All captive birds exhibited severe inbreeding (FROH = 0.352), far exceeding wild population levels (FROH = 0.131). Using the partial pedigree data of the captive sakers, we established a genetic relatedness threshold of 0.154 (95% CI: 0.096-0.211) to identify cases of related dyads (both full and half-siblings). At this threshold, 18.3% of captive dyads showed relatedness, with asymmetric genetic contributions between pairs, reflecting a functionally small breeding flock. To avoid risks from releasing admixed or inbred individuals, we recommend excluding introgressed birds, strategically pairing purebreds, and sourcing new founders from genetically validated wild sources, especially underrepresented Central Asian lineages. Applying this genomic framework, we demonstrate its role in safeguarding genetic integrity and preventing genetic erosion in conservation breeding programmes, thereby establishing a standard for genomic-led ex-situ conservation.

genomics↗

bioRxiv2020

White pupae genes in the Tephritids Ceratitis capitata, Bactrocera dorsalis and Zeugodacus cucurbitae: a story of parallel mutations

Mass releases of sterilized male insects, in the frame of sterile insect technique programs, have helped suppress insect pest populations since the 1950s. In the major horticultural pests Bactrocera dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae, a key phenotype white pupae (wp) has been used for decades to selectively remove females before releases, yet the gene responsible remained unknown. Here we use classical and modern genetic approaches to identify and functionally characterize causal wp− mutations in these distantly related fruit fly species. We find that the wp phenotype is produced by parallel mutations in a single, conserved gene. CRISPR/Cas9-mediated knockout of the wp gene leads to the rapid generation of novel white pupae strains in C. capitata and B. tryoni. The conserved phenotype and independent nature of the wp− mutations suggest that this technique can provide a generic approach to produce sexing strains in other major medical and agricultural insect pests.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2018

GenPipes: an open-source framework for distributed and scalable genomic analyses

With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.

bioinformatics↗